diff --git a/tests/test_evaluate.py b/tests/test_evaluate.py index ec177393b8ed0ff7c2aa8eb6648276c9cc929a53..712f75558a1c88fb20e06f9ea36cdfa2d1f40696 100644 --- a/tests/test_evaluate.py +++ b/tests/test_evaluate.py @@ -83,19 +83,7 @@ def test_no_call(BLANK_NA12878): assert BLANK_NA12878['alleles_no_call'] == 8 -@pytest.fixture(scope='module') -def NA12878_BLANK(): - filename = 'tests/cases/gatk.vcf.gz' - call = VCF(filename, gts012=True) - positive = VCF(filename, gts012=True) - d, disc = site_concordancy(call, positive, call_samples=['NA12878'], - positive_samples=['BLANK'], - min_gq=30, min_dp=20) - return d - - -@pytest.fixture(scope='module') -def NA12878_call_truncated(): +def test_truncated_call_file(): """ When the call set is truncated, i.e. is missing variants which are present in the positive vcf file """ @@ -106,17 +94,10 @@ def NA12878_call_truncated(): d, disc = site_concordancy(call, positive, call_samples=['NA12878'], positive_samples=['BLANK'], min_gq=30, min_dp=20) - return d - - -def test_truncated_called_no_call(NA12878_call_truncated): - """ Variants which are missing from the call vcf count towards - alleles_no_call """ - assert NA12878_call_truncated['alleles_no_call'] == 12 + assert d['alleles_no_call'] == 12 -@pytest.fixture(scope='module') -def NA12878_positive_truncated(): +def test_truncated_positive_file(): """ When the positive set is truncated, i.e. the called vcf file contains variants which are absent from the positive vcf file """ filename = 'tests/cases/gatk.vcf.gz' @@ -126,16 +107,10 @@ def NA12878_positive_truncated(): d, disc = site_concordancy(call, positive, call_samples=['NA12878'], positive_samples=['BLANK'], min_gq=30, min_dp=20) - return d - - -def test_truncated_positive_no_call(NA12878_positive_truncated): - """ Variants which are missing from the positive vcf do not count towards - alleles_no_call """ - assert NA12878_positive_truncated['alleles_no_call'] == 0 + assert d['alleles_no_call'] == 0 -def test_phased_positive(): +def test_phased_positive_file(): """ Test error message when the positive vcf contains phased variants """ filename = 'tests/cases/gatk.vcf.gz' phased = 'tests/cases/dummy_phased_blank.vcf.gz' @@ -147,7 +122,7 @@ def test_phased_positive(): positive_samples=['BLANK']) -def test_phased_call(): +def test_phased_call_file(): """ Test error message when the call vcf contains phased variants """ filename = 'tests/cases/gatk.vcf.gz' phased = 'tests/cases/dummy_phased_blank.vcf.gz'